{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,16]],"date-time":"2026-10-16T03:14:16Z","timestamp":1792120456674,"version":"4.4.0"},"reference-count":89,"publisher":"Elsevier BV","license":[{"start":{"date-parts":[[2025,8,1]],"date-time":"2025-08-01T00:00:00Z","timestamp":1754006400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2025,8,1]],"date-time":"2025-08-01T00:00:00Z","timestamp":1754006400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2025,5,22]],"date-time":"2025-05-22T00:00:00Z","timestamp":1747872000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001773","name":"University of New South Wales","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001773","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Experimental Eye Research"],"published-print":{"date-parts":[[2025,8]]},"DOI":"10.1016\/j.exer.2025.110425","type":"journal-article","created":{"date-parts":[[2025,5,22]],"date-time":"2025-05-22T02:39:52Z","timestamp":1747881592000},"page":"110425","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":8,"special_numbering":"C","title":["Whole genome sequencing-based prediction of antibiotic-resistance of ocular Staphylococcus aureus across six continents"],"prefix":"10.1016","volume":"257","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9134-5124","authenticated-orcid":false,"given":"Jiawei","family":"Shen","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Muhammad","family":"Yasir","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3842-7563","authenticated-orcid":false,"given":"Mark","family":"Willcox","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"issue":"3","key":"10.1016\/j.exer.2025.110425_bib1","doi-asserted-by":"crossref","DOI":"10.1128\/mBio.00444-16","article-title":"Whole-genome sequencing for routine pathogen surveillance in public health: a population snapshot of invasive Staphylococcus aureus in Europe","volume":"7","author":"Aanensen","year":"2016","journal-title":"mBio"},{"issue":"11","key":"10.1016\/j.exer.2025.110425_bib2","doi-asserted-by":"crossref","DOI":"10.3390\/pathogens11111354","article-title":"The relationship between ciprofloxacin resistance and genotypic changes in S. aureus ocular isolates","volume":"11","author":"Afzal","year":"2022","journal-title":"Pathogens"},{"issue":"8","key":"10.1016\/j.exer.2025.110425_bib3","article-title":"Genomics of Staphylococcus aureus strains isolated from infectious and non-infectious ocular conditions","volume":"11","author":"Afzal","year":"2022","journal-title":"Antibiotics (Basel)"},{"issue":"6","key":"10.1016\/j.exer.2025.110425_bib4","doi-asserted-by":"crossref","first-page":"1982","DOI":"10.4103\/ijo.IJO_2915_21","article-title":"Spectrum of bacterial keratitis in North India: a retrospective analysis of six years at a tertiary care eye center","volume":"70","author":"Ahmed","year":"2022","journal-title":"Indian J. Ophthalmol."},{"issue":"D1","key":"10.1016\/j.exer.2025.110425_bib5","doi-asserted-by":"crossref","first-page":"D690","DOI":"10.1093\/nar\/gkac920","article-title":"CARD 2023: expanded curation, support for machine learning, and resistome prediction at the comprehensive antibiotic resistance database","volume":"51","author":"Alcock","year":"2023","journal-title":"Nucleic Acids Res."},{"issue":"8","key":"10.1016\/j.exer.2025.110425_bib6","doi-asserted-by":"crossref","first-page":"5005","DOI":"10.1007\/s11033-014-3367-3","article-title":"Staphylococcus aureus Mobile genetic elements","volume":"41","author":"Alibayov","year":"2014","journal-title":"Mol. Biol. Rep."},{"key":"10.1016\/j.exer.2025.110425_bib7","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1016\/j.ajo.2023.06.016","article-title":"Microbiology of eye infections at the Massachusetts eye and ear: an 8-Year retrospective review combined with genomic epidemiology","volume":"255","author":"Andre","year":"2023","journal-title":"Am. J. Ophthalmol."},{"issue":"5","key":"10.1016\/j.exer.2025.110425_bib8","doi-asserted-by":"crossref","first-page":"439","DOI":"10.1001\/jamaophthalmol.2020.0155","article-title":"Trends in antibiotic resistance among ocular microorganisms in the United States from 2009 to 2018","volume":"138","author":"Asbell","year":"2020","journal-title":"JAMA Ophthalmol."},{"issue":"1","key":"10.1016\/j.exer.2025.110425_bib9","doi-asserted-by":"crossref","DOI":"10.1016\/j.diagmicrobio.2023.116069","article-title":"Antibiotic resistance of bacterial pathogens isolated from the conjunctiva in the antibiotic resistance monitoring in ocular micRoorganisms (ARMOR) surveillance study (2009-2021)","volume":"108","author":"Asbell","year":"2024","journal-title":"Diagn. Microbiol. Infect. Dis."},{"issue":"1","key":"10.1016\/j.exer.2025.110425_bib10","doi-asserted-by":"crossref","DOI":"10.1128\/msystems.00774-19","article-title":"Prediction of acquired antimicrobial resistance for multiple bacterial species using neural networks","volume":"5","author":"Aytan-Aktug","year":"2020","journal-title":"mSystems"},{"issue":"4","key":"10.1016\/j.exer.2025.110425_bib11","doi-asserted-by":"crossref","DOI":"10.3390\/microorganisms12040787","article-title":"Bacterial and fungal keratitis in a tertiary care hospital from Romania","volume":"12","author":"Balasoiu","year":"2024","journal-title":"Microorganisms"},{"issue":"12","key":"10.1016\/j.exer.2025.110425_bib12","doi-asserted-by":"crossref","first-page":"3491","DOI":"10.1093\/jac\/dkaa345","article-title":"ResFinder 4.0 for predictions of phenotypes from genotypes","volume":"75","author":"Bortolaia","year":"2020","journal-title":"J. Antimicrob. Chemother."},{"key":"10.1016\/j.exer.2025.110425_bib13","article-title":"Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and","volume":"6","author":"Bradley","year":"2015","journal-title":"Mycobacterium tuberculosis. Nat Commun."},{"key":"10.1016\/j.exer.2025.110425_bib14","doi-asserted-by":"crossref","DOI":"10.1016\/j.drup.2024.101147","article-title":"Mechanism of staphylococcal resistance to clinically relevant antibiotics","volume":"77","author":"Brdova","year":"2024","journal-title":"Drug Resist. Updates"},{"key":"10.1016\/j.exer.2025.110425_bib15","doi-asserted-by":"crossref","first-page":"29","DOI":"10.4137\/OED.S4866","article-title":"A European perspective on topical ophthalmic antibiotics: current and evolving options","volume":"3","author":"Bremond-Gignac","year":"2011","journal-title":"Ophthalmol. Eye Dis."},{"issue":"4","key":"10.1016\/j.exer.2025.110425_bib16","doi-asserted-by":"crossref","first-page":"258","DOI":"10.1111\/j.1444-0938.2007.00154.x","article-title":"Resistance to ocular antibiotics: an overview","volume":"90","author":"Brown","year":"2007","journal-title":"Clin. Exp. Optom."},{"issue":"1","key":"10.1016\/j.exer.2025.110425_bib17","doi-asserted-by":"crossref","first-page":"70","DOI":"10.1016\/0147-619X(91)90008-K","article-title":"4',4'' adenyltransferase activity on conjugative plasmids isolated from Staphylococcus aureus is encoded on an integrated copy of pUB110","volume":"25","author":"Byrne","year":"1991","journal-title":"Plasmid"},{"issue":"3","key":"10.1016\/j.exer.2025.110425_bib18","doi-asserted-by":"crossref","first-page":"258","DOI":"10.1111\/ceo.14377","article-title":"Antimicrobial resistance in ocular infection: a review","volume":"52","author":"Cabrera-Aguas","year":"2024","journal-title":"Clin. Exp. Ophthalmol."},{"key":"10.1016\/j.exer.2025.110425_bib19","doi-asserted-by":"crossref","first-page":"421","DOI":"10.1186\/1471-2105-10-421","article-title":"BLAST+: architecture and applications","volume":"10","author":"Camacho","year":"2009","journal-title":"BMC Bioinf."},{"issue":"7","key":"10.1016\/j.exer.2025.110425_bib20","doi-asserted-by":"crossref","first-page":"3895","DOI":"10.1128\/AAC.02412-14","article-title":"In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing","volume":"58","author":"Carattoli","year":"2014","journal-title":"Antimicrob. Agents Chemother."},{"issue":"6","key":"10.1016\/j.exer.2025.110425_bib21","doi-asserted-by":"crossref","first-page":"698","DOI":"10.1097\/ICO.0000000000000431","article-title":"Antibiotic resistance in the treatment of Staphylococcus aureus keratitis: a 20-Year review","volume":"34","author":"Chang","year":"2015","journal-title":"Cornea"},{"issue":"9","key":"10.1016\/j.exer.2025.110425_bib22","doi-asserted-by":"crossref","first-page":"1622","DOI":"10.1016\/j.ophtha.2006.12.011","article-title":"Clinical efficacy of moxifloxacin in the treatment of bacterial keratitis: a randomized clinical trial","volume":"114","author":"Constantinou","year":"2007","journal-title":"Ophthalmology"},{"key":"10.1016\/j.exer.2025.110425_bib23","first-page":"48","article-title":"Australian group on antimicrobial resistance (AGAR) Australian Staphylococcus aureus surveillance outcome program (ASSOP) bloodstream infection annual report 2023","volume":"2024","author":"Coombs","year":"2018","journal-title":"Commun. Dis. Intell."},{"issue":"1","key":"10.1016\/j.exer.2025.110425_bib24","doi-asserted-by":"crossref","first-page":"60","DOI":"10.1076\/ceyr.23.1.60.5417","article-title":"The effectiveness of tobramycin and ocuflox in a prophylaxis model of staphylococcus keratitis","volume":"23","author":"Dajcs","year":"2001","journal-title":"Curr. Eye Res."},{"issue":"5","key":"10.1016\/j.exer.2025.110425_bib25","doi-asserted-by":"crossref","DOI":"10.3390\/microorganisms12050984","article-title":"Antibiotic resistance profiles in eye infections: a local concern with a retrospective focus on a large hospital in northern Italy","volume":"12","author":"Drago","year":"2024","journal-title":"Microorganisms"},{"key":"10.1016\/j.exer.2025.110425_bib26","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1016\/j.plasmid.2018.05.001","article-title":"Mobile macrolide resistance genes in staphylococci","volume":"99","author":"Fessler","year":"2018","journal-title":"Plasmid"},{"issue":"4","key":"10.1016\/j.exer.2025.110425_bib27","doi-asserted-by":"crossref","first-page":"399","DOI":"10.1001\/archophthalmol.2011.45","article-title":"Topical fluoroquinolone use as a risk factor for in vitro fluoroquinolone resistance in ocular cultures","volume":"129","author":"Fintelmann","year":"2011","journal-title":"Arch. Ophthalmol."},{"issue":"12","key":"10.1016\/j.exer.2025.110425_bib28","doi-asserted-by":"crossref","first-page":"5406","DOI":"10.1128\/AAC.00580-10","article-title":"LmrS is a multidrug efflux pump of the major facilitator superfamily from Staphylococcus aureus","volume":"54","author":"Floyd","year":"2010","journal-title":"Antimicrob. Agents Chemother."},{"issue":"10","key":"10.1016\/j.exer.2025.110425_bib29","doi-asserted-by":"crossref","first-page":"2601","DOI":"10.1093\/jac\/dkad238","article-title":"The native ABC-F proteins of Staphylococcus aureus do not contribute to intrinsic resistance against ribosome-targeting antibacterial drugs","volume":"78","author":"Galarion","year":"2023","journal-title":"J. Antimicrob. Chemother."},{"issue":"4","key":"10.1016\/j.exer.2025.110425_bib30","doi-asserted-by":"crossref","first-page":"378","DOI":"10.1136\/bjo.84.4.378","article-title":"Fluoroquinolone and fortified antibiotics for treating bacterial corneal ulcers","volume":"84","author":"Gangopadhyay","year":"2000","journal-title":"Br. J. Ophthalmol."},{"issue":"8","key":"10.1016\/j.exer.2025.110425_bib31","doi-asserted-by":"crossref","first-page":"777","DOI":"10.1111\/j.1469-0691.2007.01749.x","article-title":"Distribution and expression of macrolide resistance genes in coagulase-negative staphylococci","volume":"13","author":"Gatermann","year":"2007","journal-title":"Clin. Microbiol. Infect."},{"issue":"2","key":"10.1016\/j.exer.2025.110425_bib32","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1099\/00222615-24-2-139","article-title":"Chromosome- and plasmid-mediated gentamicin resistance in Staphylococcus aureus encoded by Tn4001","volume":"24","author":"Gillespie","year":"1987","journal-title":"J. Med. Microbiol."},{"issue":"5","key":"10.1016\/j.exer.2025.110425_bib33","doi-asserted-by":"crossref","first-page":"565","DOI":"10.2217\/fmb.09.30","article-title":"Genetics of antimicrobial resistance in Staphylococcus aureus","volume":"4","author":"Jensen","year":"2009","journal-title":"Future Microbiol."},{"issue":"5","key":"10.1016\/j.exer.2025.110425_bib34","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0250975","article-title":"Genomics of Staphylococcus aureus ocular isolates","volume":"16","author":"Johnson","year":"2021","journal-title":"PLoS One"},{"key":"10.1016\/j.exer.2025.110425_bib35","doi-asserted-by":"crossref","first-page":"124","DOI":"10.12688\/wellcomeopenres.14826.1","article-title":"Open-access bacterial population genomics: BIGSdb software, the PubMLST.org website and their applications","volume":"3","author":"Jolley","year":"2018","journal-title":"Wellcome Open Res."},{"issue":"4","key":"10.1016\/j.exer.2025.110425_bib36","doi-asserted-by":"crossref","first-page":"1276","DOI":"10.1128\/AAC.50.4.1276-1281.2006","article-title":"MepR, a repressor of the Staphylococcus aureus MATE family multidrug efflux pump MepA, is a substrate-responsive regulatory protein","volume":"50","author":"Kaatz","year":"2006","journal-title":"Antimicrob. Agents Chemother."},{"key":"10.1016\/j.exer.2025.110425_bib37","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1111\/j.1749-6632.2011.06315.x","article-title":"Macrolide antibiotics in the ribosome exit tunnel: species-specific binding and action","volume":"1241","author":"Kannan","year":"2011","journal-title":"Ann. N. Y. Acad. Sci."},{"key":"10.1016\/j.exer.2025.110425_bib38","doi-asserted-by":"crossref","DOI":"10.1016\/j.exer.2021.108764","article-title":"Characterization of antibiotic resistance and virulence genes of ocular methicillin-resistant Staphylococcus aureus strains through complete genome analysis","volume":"212","author":"Kathirvel","year":"2021","journal-title":"Exp. Eye Res."},{"issue":"4","key":"10.1016\/j.exer.2025.110425_bib39","doi-asserted-by":"crossref","first-page":"772","DOI":"10.1093\/molbev\/mst010","article-title":"MAFFT multiple sequence alignment software version 7: improvements in performance and usability","volume":"30","author":"Katoh","year":"2013","journal-title":"Mol. Biol. Evol."},{"issue":"1","key":"10.1016\/j.exer.2025.110425_bib40","doi-asserted-by":"crossref","first-page":"362","DOI":"10.1167\/iovs.09-3933","article-title":"Bacterial susceptibility to topical antimicrobials and clinical outcome in bacterial keratitis","volume":"51","author":"Kaye","year":"2010","journal-title":"Investig. Ophthalmol. Vis. Sci."},{"key":"10.1016\/j.exer.2025.110425_bib41","doi-asserted-by":"crossref","first-page":"341","DOI":"10.1146\/annurev.ge.15.120181.002013","article-title":"Transposable elements in prokaryotes","volume":"15","author":"Kleckner","year":"1981","journal-title":"Annu. Rev. Genet."},{"issue":"4","key":"10.1016\/j.exer.2025.110425_bib42","doi-asserted-by":"crossref","first-page":"541","DOI":"10.33073\/pjm-2019-056","article-title":"Epidemiology, drug resistance, and virulence of Staphylococcus aureus isolated from ocular infections in Polish patients","volume":"68","author":"Klos","year":"2019","journal-title":"Pol. J. Microbiol."},{"issue":"9","key":"10.1016\/j.exer.2025.110425_bib43","doi-asserted-by":"crossref","first-page":"401","DOI":"10.1016\/j.tig.2014.07.003","article-title":"Whole-genome sequencing to control antimicrobial resistance","volume":"30","author":"Koser","year":"2014","journal-title":"Trends Genet."},{"issue":"2","key":"10.1016\/j.exer.2025.110425_bib44","first-page":"423","article-title":"Evidence for two mechanisms of plasmid transfer in mixed cultures of Staphylococcus aureus","volume":"119","author":"Lacey","year":"1980","journal-title":"J. Gen. Microbiol."},{"issue":"10","key":"10.1016\/j.exer.2025.110425_bib45","doi-asserted-by":"crossref","first-page":"1381","DOI":"10.1093\/cid\/cis189","article-title":"Relationship of in vitro susceptibility to moxifloxacin and in vivo clinical outcome in bacterial keratitis","volume":"54","author":"Lalitha","year":"2012","journal-title":"Clin. Infect. Dis."},{"issue":"9","key":"10.1016\/j.exer.2025.110425_bib46","doi-asserted-by":"crossref","first-page":"1707","DOI":"10.18240\/ijo.2024.09.19","article-title":"Five-year analysis of isolated pathogens and antibiotic resistance of ocular infections from two large tertiary comprehensive hospitals in east China","volume":"17","author":"Li","year":"2024","journal-title":"Int. J. Ophthalmol."},{"key":"10.1016\/j.exer.2025.110425_bib47","doi-asserted-by":"crossref","first-page":"548","DOI":"10.1016\/j.meegid.2013.04.017","article-title":"Evolution of Staphylococcus aureus and MRSA during outbreaks","volume":"21","author":"Lindsay","year":"2014","journal-title":"Infect. Genet. Evol."},{"issue":"11","key":"10.1016\/j.exer.2025.110425_bib48","doi-asserted-by":"crossref","DOI":"10.1128\/jcm.00617-23","article-title":"Direct prediction of carbapenem resistance in Pseudomonas aeruginosa by whole genome sequencing and metagenomic sequencing","volume":"61","author":"Liu","year":"2023","journal-title":"J. Clin. Microbiol."},{"issue":"9","key":"10.1016\/j.exer.2025.110425_bib49","doi-asserted-by":"crossref","first-page":"1265","DOI":"10.1172\/JCI18535","article-title":"Antimicrobial resistance: the example of Staphylococcus aureus","volume":"111","author":"Lowy","year":"2003","journal-title":"J. Clin. Investig."},{"issue":"1","key":"10.1016\/j.exer.2025.110425_bib50","doi-asserted-by":"crossref","DOI":"10.1128\/spectrum.00234-24","article-title":"Spectrum of bacterial keratitis at a tertiary eye center in Indonesia","volume":"13","author":"Lutfiamida","year":"2025","journal-title":"Microbiol. Spectr."},{"issue":"2","key":"10.1016\/j.exer.2025.110425_bib51","doi-asserted-by":"crossref","first-page":"287","DOI":"10.1016\/S0378-1097(03)00134-4","article-title":"Characteristic expression of three genes, msr(A), mph(C) and erm(Y), that confer resistance to macrolide antibiotics on Staphylococcus aureus","volume":"220","author":"Matsuoka","year":"2003","journal-title":"FEMS Microbiol. Lett."},{"issue":"15","key":"10.1016\/j.exer.2025.110425_bib52","doi-asserted-by":"crossref","DOI":"10.3390\/ijms23158088","article-title":"Molecular mechanisms of drug resistance in Staphylococcus aureus","volume":"23","author":"Mlynarczyk-Bonikowska","year":"2022","journal-title":"Int. J. Mol. Sci."},{"issue":"3","key":"10.1016\/j.exer.2025.110425_bib53","first-page":"700","article-title":"Prediction of antibiotic resistance from antibiotic resistance genes detected in antibiotic-resistant commensal Escherichia coli using PCR or WGS","volume":"72","author":"Moran","year":"2017","journal-title":"J. Antimicrob. Chemother."},{"key":"10.1016\/j.exer.2025.110425_bib54","first-page":"165","article-title":"Staphylococcus aureus eye infections in two Indian hospitals: emergence of ST772 as a major clone","volume":"6","author":"Nadig","year":"2012","journal-title":"Clin. Ophthalmol."},{"issue":"7","key":"10.1016\/j.exer.2025.110425_bib55","doi-asserted-by":"crossref","DOI":"10.1128\/MRA.00077-21","article-title":"Draft genome sequence of the community-associated Staphylococcus aureus sequence type 88 strain LVP-7, isolated from an ocular infection","volume":"10","author":"Nadig","year":"2021","journal-title":"Microbiol. Resou. Announc."},{"issue":"6","key":"10.1016\/j.exer.2025.110425_bib56","doi-asserted-by":"crossref","first-page":"1345","DOI":"10.1128\/AAC.38.6.1345","article-title":"Quinolone resistance mediated by norA: physiologic characterization and relationship to flqB, a quinolone resistance locus on the Staphylococcus aureus chromosome","volume":"38","author":"Ng","year":"1994","journal-title":"Antimicrob. Agents Chemother."},{"issue":"1","key":"10.1016\/j.exer.2025.110425_bib57","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1016\/0147-619X(79)90010-6","article-title":"Penicillinase plasmids of staphylococcus aureus: restriction-deletion maps","volume":"2","author":"Novick","year":"1979","journal-title":"Plasmid"},{"issue":"3","key":"10.1016\/j.exer.2025.110425_bib58","doi-asserted-by":"crossref","first-page":"450","DOI":"10.1093\/jac\/dki492","article-title":"Diversity and evolution of blaZ from Staphylococcus aureus and coagulase-negative staphylococci","volume":"57","author":"Olsen","year":"2006","journal-title":"J. Antimicrob. Chemother."},{"issue":"6","key":"10.1016\/j.exer.2025.110425_bib59","doi-asserted-by":"crossref","first-page":"1243","DOI":"10.1093\/jac\/dkq106","article-title":"Evaluation of synergistic activity of bovine lactoferricin with antibiotics in corneal infection","volume":"65","author":"Oo","year":"2010","journal-title":"J. Antimicrob. Chemother."},{"issue":"22","key":"10.1016\/j.exer.2025.110425_bib60","doi-asserted-by":"crossref","first-page":"3691","DOI":"10.1093\/bioinformatics\/btv421","article-title":"Roary: rapid large-scale prokaryote pan genome analysis","volume":"31","author":"Page","year":"2015","journal-title":"Bioinformatics"},{"key":"10.1016\/j.exer.2025.110425_bib61","doi-asserted-by":"crossref","first-page":"577","DOI":"10.1146\/annurev-biochem-060614-034516","article-title":"Mechanisms of methicillin resistance in Staphylococcus aureus","volume":"84","author":"Peacock","year":"2015","journal-title":"Annu. Rev. Biochem."},{"issue":"3","key":"10.1016\/j.exer.2025.110425_bib62","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0009490","article-title":"FastTree 2--approximately maximum-likelihood trees for large alignments","volume":"5","author":"Price","year":"2010","journal-title":"PLoS One"},{"issue":"6","key":"10.1016\/j.exer.2025.110425_bib63","doi-asserted-by":"crossref","first-page":"151","DOI":"10.1016\/j.drup.2010.08.003","article-title":"Aminoglycoside modifying enzymes","volume":"13","author":"Ramirez","year":"2010","journal-title":"Drug Resist. Updates"},{"issue":"3","key":"10.1016\/j.exer.2025.110425_bib64","doi-asserted-by":"crossref","first-page":"228","DOI":"10.1016\/S0924-8579(03)00218-8","article-title":"Msr(A) and related macrolide\/streptogramin resistance determinants: incomplete transporters?","volume":"22","author":"Reynolds","year":"2003","journal-title":"Int. J. Antimicrob. Agents"},{"issue":"11","key":"10.1016\/j.exer.2025.110425_bib65","first-page":"3039","article-title":"The aacA-aphD gentamicin and kanamycin resistance determinant of Tn4001 from staphylococcus aureus: expression and nucleotide sequence analysis","volume":"133","author":"Rouch","year":"1987","journal-title":"J. Gen. Microbiol."},{"issue":"6","key":"10.1016\/j.exer.2025.110425_bib66","doi-asserted-by":"crossref","first-page":"961","DOI":"10.1111\/j.1365-2958.1990.tb00669.x","article-title":"Tn552, a novel transposable element from Staphylococcus aureus","volume":"4","author":"Rowland","year":"1990","journal-title":"Mol. Microbiol."},{"issue":"1","key":"10.1016\/j.exer.2025.110425_bib67","doi-asserted-by":"crossref","first-page":"193","DOI":"10.1186\/s13104-024-06851-3","article-title":"Prevalence and antimicrobial susceptibility patterns of bacteria colonizing the external ocular surfaces of patients undergoing ocular surgeries at bugando medical center in Mwanza, Tanzania","volume":"17","author":"Rukyaa","year":"2024","journal-title":"BMC Res. Notes"},{"issue":"5","key":"10.1016\/j.exer.2025.110425_bib68","first-page":"581","article-title":"Surveillance of the activity of aminoglycosides and fluoroquinolones against ophthalmic pathogens from Europe in 2010-2011","volume":"41","author":"Sanfilippo","year":"2016","journal-title":"Curr. Eye Res."},{"issue":"1","key":"10.1016\/j.exer.2025.110425_bib69","doi-asserted-by":"crossref","first-page":"54","DOI":"10.1093\/oxfordjournals.bmb.a071948","article-title":"Genetics and evolution of antibiotic resistance","volume":"40","author":"Saunders","year":"1984","journal-title":"Br. Med. Bull."},{"issue":"1","key":"10.1016\/j.exer.2025.110425_bib70","doi-asserted-by":"crossref","first-page":"108","DOI":"10.1111\/nyas.13310","article-title":"Challenges and opportunities for whole-genome sequencing-based surveillance of antibiotic resistance","volume":"1388","author":"Schurch","year":"2017","journal-title":"Ann. N. Y. Acad. Sci."},{"issue":"14","key":"10.1016\/j.exer.2025.110425_bib71","doi-asserted-by":"crossref","first-page":"2068","DOI":"10.1093\/bioinformatics\/btu153","article-title":"Prokka: rapid prokaryotic genome annotation","volume":"30","author":"Seemann","year":"2014","journal-title":"Bioinformatics"},{"issue":"11","key":"10.1016\/j.exer.2025.110425_bib72","doi-asserted-by":"crossref","first-page":"3110","DOI":"10.1038\/s41433-020-01378-w","article-title":"Infectious keratitis: trends in microbiological and antibiotic sensitivity patterns","volume":"35","author":"Soleimani","year":"2021","journal-title":"Eye (Lond)."},{"issue":"8","key":"10.1016\/j.exer.2025.110425_bib73","doi-asserted-by":"crossref","first-page":"1229","DOI":"10.1038\/eye.2017.55","article-title":"Twelve-year analysis of microbial keratitis trends at a UK tertiary hospital","volume":"31","author":"Tan","year":"2017","journal-title":"Eye (Lond)."},{"issue":"1","key":"10.1016\/j.exer.2025.110425_bib74","doi-asserted-by":"crossref","first-page":"212","DOI":"10.1186\/s12886-017-0612-2","article-title":"Bacterial profile of ocular infections: a systematic review","volume":"17","author":"Teweldemedhin","year":"2017","journal-title":"BMC Ophthalmol."},{"issue":"4","key":"10.1016\/j.exer.2025.110425_bib75","doi-asserted-by":"crossref","first-page":"1084","DOI":"10.1038\/s41433-020-01339-3","article-title":"Infectious keratitis: an update on epidemiology, causative microorganisms, risk factors, and antimicrobial resistance","volume":"35","author":"Ting","year":"2021","journal-title":"Eye (Lond)."},{"issue":"3","key":"10.1016\/j.exer.2025.110425_bib76","doi-asserted-by":"crossref","first-page":"328","DOI":"10.1136\/bjophthalmol-2020-316128","article-title":"12-year analysis of incidence, microbiological profiles and in vitro antimicrobial susceptibility of infectious keratitis: the Nottingham infectious keratitis study","volume":"105","author":"Ting","year":"2021","journal-title":"Br. J. Ophthalmol."},{"issue":"7","key":"10.1016\/j.exer.2025.110425_bib77","doi-asserted-by":"crossref","first-page":"2395","DOI":"10.1128\/JB.187.7.2395-2405.2005","article-title":"MgrA is a multiple regulator of two new efflux pumps in Staphylococcus aureus","volume":"187","author":"Truong-Bolduc","year":"2005","journal-title":"J. Bacteriol."},{"issue":"3","key":"10.1016\/j.exer.2025.110425_bib78","doi-asserted-by":"crossref","first-page":"1104","DOI":"10.1128\/AAC.50.3.1104-1107.2006","article-title":"NorC, a new efflux pump regulated by MgrA of Staphylococcus aureus","volume":"50","author":"Truong-Bolduc","year":"2006","journal-title":"Antimicrob. Agents Chemother."},{"issue":"7","key":"10.1016\/j.exer.2025.110425_bib79","doi-asserted-by":"crossref","first-page":"1823","DOI":"10.1128\/JB.06503-11","article-title":"Reduced aeration affects the expression of the NorB efflux pump of Staphylococcus aureus by posttranslational modification of MgrA","volume":"194","author":"Truong-Bolduc","year":"2012","journal-title":"J. Bacteriol."},{"key":"10.1016\/j.exer.2025.110425_bib80","doi-asserted-by":"crossref","DOI":"10.1016\/j.preteyeres.2021.101031","article-title":"Bacterial keratitis: identifying the areas of clinical uncertainty","volume":"89","author":"Tuft","year":"2022","journal-title":"Prog. Retin. Eye Res."},{"issue":"9","key":"10.1016\/j.exer.2025.110425_bib81","doi-asserted-by":"crossref","first-page":"1535","DOI":"10.1128\/AAC.33.9.1535","article-title":"Cloning and expression of the norA gene for fluoroquinolone resistance in Staphylococcus aureus","volume":"33","author":"Ubukata","year":"1989","journal-title":"Antimicrob. Agents Chemother."},{"issue":"2","key":"10.1016\/j.exer.2025.110425_bib82","doi-asserted-by":"crossref","DOI":"10.1128\/genomeA.00168-14","article-title":"Draft genome sequences of Staphylococcus aureus AMRF1 (ST22) and AMRF2 (ST672), ocular methicillin-resistant isolates","volume":"2","author":"Velusamy","year":"2014","journal-title":"Genome Announc."},{"key":"10.1016\/j.exer.2025.110425_bib83","first-page":"44","article-title":"Bacterial ocular surveillance system (BOSS) Sydney, Australia 2017-2018","author":"Watson","year":"2018","journal-title":"Commun. Dis. Intell."},{"issue":"11","key":"10.1016\/j.exer.2025.110425_bib84","doi-asserted-by":"crossref","first-page":"3970","DOI":"10.1128\/JCM.40.11.3970-3975.2002","article-title":"mecA gene is widely disseminated in Staphylococcus aureus population","volume":"40","author":"Wielders","year":"2002","journal-title":"J. Clin. Microbiol."},{"issue":"11","key":"10.1016\/j.exer.2025.110425_bib85","doi-asserted-by":"crossref","first-page":"637","DOI":"10.1038\/s41579-020-0386-z","article-title":"Target protection as a key antibiotic resistance mechanism","volume":"18","author":"Wilson","year":"2020","journal-title":"Nat. Rev. Microbiol."},{"issue":"1","key":"10.1016\/j.exer.2025.110425_bib86","doi-asserted-by":"crossref","DOI":"10.1038\/s41598-024-77723-w","article-title":"Microbial profile and associated factors of external ocular bacterial and fungal infections in arba minch general hospital: a cross-sectional study","volume":"14","author":"Woldemariam","year":"2024","journal-title":"Sci. Rep."},{"issue":"3","key":"10.1016\/j.exer.2025.110425_bib87","doi-asserted-by":"crossref","first-page":"554","DOI":"10.1248\/bpb.29.554","article-title":"Gene cloning and characterization of SdrM, a chromosomally-encoded multidrug efflux pump, from Staphylococcus aureus","volume":"29","author":"Yamada","year":"2006","journal-title":"Biol. Pharm. Bull."},{"issue":"11","key":"10.1016\/j.exer.2025.110425_bib88","doi-asserted-by":"crossref","first-page":"2640","DOI":"10.1093\/jac\/dks261","article-title":"Identification of acquired antimicrobial resistance genes","volume":"67","author":"Zankari","year":"2012","journal-title":"J. Antimicrob. Chemother."},{"issue":"10","key":"10.1016\/j.exer.2025.110425_bib89","doi-asserted-by":"crossref","first-page":"2764","DOI":"10.1093\/jac\/dkx217","article-title":"PointFinder: a novel web tool for WGS-Based detection of antimicrobial resistance associated with chromosomal point mutations in bacterial pathogens","volume":"72","author":"Zankari","year":"2017","journal-title":"J. Antimicrob. Chemother."}],"container-title":["Experimental Eye Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0014483525001964?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0014483525001964?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,5,11]],"date-time":"2026-05-11T04:21:53Z","timestamp":1778473313000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S0014483525001964"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,8]]},"references-count":89,"alternative-id":["S0014483525001964"],"URL":"https:\/\/doi.org\/10.1016\/j.exer.2025.110425","relation":{},"ISSN":["0014-4835"],"issn-type":[{"value":"0014-4835","type":"print"}],"subject":[],"published":{"date-parts":[[2025,8]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Whole genome sequencing-based prediction of antibiotic-resistance of ocular Staphylococcus aureus across six continents","name":"articletitle","label":"Article Title"},{"value":"Experimental Eye Research","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.exer.2025.110425","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2025 The Authors. Published by Elsevier Ltd.","name":"copyright","label":"Copyright"}],"article-number":"110425"}}